segger_dev icon indicating copy to clipboard operation
segger_dev copied to clipboard

Updating Xenium explorer.

Open EliHei2 opened this issue 11 months ago • 0 comments

Thank you @senbaikang for your multi-GPU solution!  

Hi @EliHei2 I realized that the seg2explorer function is kind of out-of-date: https://www.10xgenomics.com/support/software/xenium-onboard-analysis/latest/advanced/xoa-output-zarr

The cells.zarr.zip file cannot be visualized with the XOA v3.2 data. My solution is to extract nuclei and cell coordinates as GEOJSON files and use Xenium Ranger to import them (https://www.10xgenomics.com/support/software/xenium-ranger/latest/analysis/inputs/segmentation-inputs), but that's pretty time consuming and will take additional ~10 G of hard drive space for each sample. If you can fix this, it would be wonderful!

Thank you! Qijie

Originally posted by @MiracleEaTu in #83

EliHei2 avatar Jan 30 '25 18:01 EliHei2